Rootlets-based registration to PAM50 template

Spinal rootlets-informed registration to the template

Installation

Dependencies

• Spinal cord Toolbox v6.5
• Python 3.9

Datasets

• Spine Generic Multi-subject dataset version r20250310
• Spinal Cord Head Positions dataset version v1.1.1

Installation

Clone Github repository

git clone [email protected]:sct-pipeline/rootlets-informed-reg2template.git
cd rootlets-informed-reg2template

Using SCT virtual environement

source ${SCT_DIR}/python/etc/profile.d/conda.sh
conda activate venv_sct

Inter-subject Validation

Run batch regsitration to template using rootlets and disc-based template regsitration. This will also compute spianl cord cross-sectional area in template space

  sct_run_batch -jobs -1 -path-data <PATH_DATA> -script /processing_script/process_spine_generic.sh -path-out <PATH_OUT>

Create average image of rootlets-based registration:

python average_images.py -path-data <PATH_DATA_PROCESSED> -path-file reg_rootlets -path-out <PATH_RESULTS> -exclude processing_script/exclude_spine_generic.yml 

For disc-based registration

python average_images.py -path-data <PATH_DATA_PROCESSED> -path-file reg_discs -path-out <PATH_RESULTS> -exclude processing_script/exclude_spine_generic.yml 

Morphometric analysis

python csa_analysis.py -i <PATH_RESULTS> -o <PATH_RESULTS>/results_spine_generic_csa_2024-11-21 -exclude processing_script/exclude_spine_generic.yml

Single-subject Validation

  sct_run_batch -jobs -1 -path-data <PATH_DATA> -script /processing_script/process_pmj_data.sh -path-out <PATH_OUT>

Analyse Functional Data

python analyse_func_ridge.py -i1 <rootlets_smooth_3.1_FE/thresh_zstat1_med.nii.gz> -i2 <discs_smooth_3.1_FE/thresh_zstat1_med.nii.gz> -o <PATH_OUT>